Transcription of eukaryotic genomes is more widespread than was previously anticipated and results in the production of many non–protein-coding RNAs (ncRNAs) whose functional relevance is poorly understood. Here we demonstrate that ncRNAs can counteract the encroachment of heterochromatin into neighboring euchromatin. We have identified a long ncRNA (termed BORDERLINE) that prevents spreading of the HP1 protein Swi6 and histone H3 Lys9 methylation beyond the pericentromeric repeat region of Schizosaccharomyces pombe chromosome 1. BORDERLINE RNAs act in a sequence-independent but locus-dependent manner and are processed by Dicer into short RNAs referred to as brdrRNAs. In contrast to canonical centromeric short interfering RNAs, brdrRNAs are rarely loaded onto Argonaute. Our analyses reveal an unexpected regulatory activity of ncRNAs in demarcating an epigenetically distinct chromosomal domain that could also be operational in other eukaryotes.
At a glance
Gene Expression Omnibus
- Landscape of transcription in human cells. Nature 489, 101–108 (2012). et al.
- Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453, 1239–1243 (2008). et al.
- The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008). et al.
- Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833–1837 (2002). et al.
- Establishment and maintenance of a heterochromatin domain. Science 297, 2232–2237 (2002). et al.
- RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672–676 (2004). et al.
- Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119, 789–802 (2004). et al.
- Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity. Cell 140, 666–677 (2010). et al.
- Common ground: small RNA programming and chromatin modifications. Curr. Opin. Cell Biol. 23, 258–265 (2011). &
- Heterochromatin and epigenetic control of gene expression. Science 301, 798–802 (2003). &
- Putting boundaries on silence. Cell 99, 459–462 (1999). &
- RNAi-independent heterochromatin nucleation by the stress-activated ATF/CREB family proteins. Science 304, 1971–1976 (2004). , &
- The nucleation and maintenance of heterochromatin by a histone deacetylase in fission yeast. Mol. Cell 20, 173–185 (2005). , , , &
- Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293, 1150–1155 (2001). , &
- Expression-state boundaries in the mating-type region of fission yeast. Genetics 161, 611–622 (2002). , , &
- The genome sequence of Schizosaccharomyces pombe. Nature 415, 871–880 (2002). et al.
- A heterochromatin barrier partitions the fission yeast centromere into discrete chromatin domains. Curr. Biol. 16, 119–129 (2006). , &
- A role for TFIIIC transcription factor complex in genome organization. Cell 125, 859–872 (2006). , , &
- An RNA polymerase III-dependent heterochromatin barrier at fission yeast centromere 1. PLoS ONE 2, e1099 (2007). , &
- Central role of Drosophila SU(VAR)3–9 in histone H3–K9 methylation and heterochromatic gene silencing. EMBO J. 21, 1121–1131 (2002). et al.
- Chromodomain-mediated oligomerization of HP1 suggests a nucleosome-bridging mechanism for heterochromatin assembly. Mol. Cell 41, 67–81 (2011). et al.
- Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292, 110–113 (2001). , , , &
- Heterochromatin revisited. Nat. Rev. Genet. 8, 35–46 (2007). &
- HP1(Swi6) mediates the recognition and destruction of heterochromatic RNA transcripts. Mol. Cell 47, 215–227 (2012). et al.
- TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat. Struct. Mol. Biol. 15, 1015–1023 (2008). , , &
- Dicer-independent primal RNAs trigger RNAi and heterochromatin formation. Cell 140, 504–516 (2010). &
- Small RNAs correspond to centromere heterochromatic repeats. Science 297, 1831 (2002). &
- Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat. Genet. 37, 809–819 (2005). et al.
- RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nat. Genet. 36, 1174–1180 (2004). et al.
- A Cullin E3 ubiquitin ligase complex associates with Rik1 and the Clr4 histone H3–K9 methyltransferase and is required for RNAi-mediated heterochromatin formation. RNA Biol. 2, 106–111 (2005). , , , &
- Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci. Signal. 3, ra8 (2010). , , , &
- Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. EMBO J. 31, 522–533 (2012). , &
- Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445, 666–670 (2007). , , , &
- Dynamic nature of heterochromatin highlighted by a HP1 (Swi6)-dependent gene silencing mechanism. Cell Cycle 11, 3907–3908 (2012). &
- Small RNAs in transcriptional gene silencing and genome defence. Nature 457, 413–420 (2009).
- Transcription and RNA interference in the formation of heterochromatin. Nature 447, 399–406 (2007). &
- Transcription and RNAi in heterochromatic gene silencing. Nat. Struct. Mol. Biol. 14, 1041–1048 (2007). &
- RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat. Rev. Genet. 14, 100–112 (2013). &
- Centromeric chromatin in fission yeast. Front. Biosci. 13, 3896–3905 (2008).
- Mutations derepressing silent centromeric domains in fission yeast disrupt chromosome segregation. Genes Dev. 9, 218–233 (1995). , , , &
- Heterologous modules for efficient and versatile PCR-based gene targeting in Schizosaccharomyces pombe. Yeast 14, 943–951 (1998). et al.
- Heterologous URA3MX cassettes for gene replacement in Saccharomyces cerevisiae. Yeast 15, 507–511 (1999). , &
- Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae. Yeast 21, 661–670 (2004). &
- HP1(Swi6) mediates the recognition and destruction of heterochromatic rna transcripts. Mol. Cell 47, 215–227 (2012). et al.
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009). , , &
- Tethering RITS to a nascent transcript initiates rnai- and heterochromatin-dependent gene silencing. Cell 125, 873–886 (2006). , &
- The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon. Genes Dev. 5, 2303–2314 (1991). , , &
- Nuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly. Dev. Cell 18, 102–113 (2010). et al.
- Supplementary Text and Figures (3,144.8 KB)
Supplementary Figures 1–7 and Supplementary Tables 1 and 2